Symbiont alpha-diversity - Grouped by Species

First, we look at how many Symbiodinium types (OTUs) and clades are present in each coral species:

Plot OTU and clade diversity by species

##           OTUs Clades
## Platygyra   40      4
## Favites     61      4

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Sample sizes for different coral taxa

## [1] 146
## NULL
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##   2
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Barplot by Symbiodinium Clade - Platygyra and Favites pentagona Combined barplot by clade

Barplot by Symbiodinium Hit - Platygyra and Favites pentagona Combined barplot by Hit

Symbiont alpha-diversity - Grouped by Sites (and SampleType)

Next, we look at the number of Symbiodinium types (OTUs) and clades in coral at each Kiritimati site:

OTU and Clade Diversity by Site

##        OTUs Clades Dist Subclades
## site27   67      5    1        32
## site30   87      5    1        36
## site32   26      4    1        16
## site40   10      4    1         8
## site3     7      4    2         7
## site25   14      4    2        10
## site38   19      4    2        15
## site8    47      5    3        24
## site14   10      2    3         7
## site34   56      5    3        29
## site35   86      5    3        30
## site5    23      4    5        13
## site37    7      3    5         5
## site15   31      4    6        18
## site19    5      2    6         5

##        OTUs Clades Dist Subclades
## site27   13      3    1         9
## site30    6      3    1         5
## site32   14      3    1         9
## site40    6      3    1         5
## site3     7      4    2         7
## site25   11      3    2         8
## site38    3      3    2         3
## site8     6      3    3         5
## site14    6      2    3         5
## site34   15      5    3        11
## site35   11      4    3         9
## site5    14      3    5         9
## site37    6      3    5         5
## site15    7      3    6         7

##        OTUs Clades Dist Subclades
## site27   13      4    1        11
## site30   11      3    1         7
## site32   14      3    1        11
## site40    6      3    1         5
## site3     2      2    2         2
## site25    5      3    2         4
## site38   10      2    2         7
## site8     5      2    3         5
## site14    6      2    3         5
## site34   14      4    3        10
## site35    5      2    3         3
## site5    10      3    5         8
## site37    4      3    5         3
## site15   27      4    6        15
## site19    5      2    6         5

OTU and Clade Diversity by Disturbance Level

Symbiont alpha-diversity - Grouped by Field Season

To understand how Symbiodinium diversity changes among field seasons, clade diversity is divided by field season. This includes coral-associated Symbiodinium.

OTU and Clade Diversity by Field Season

##         OTUs Clades
## KI2014    27      4
## KI2015a   18      3
## KI2015b   33      4
## KI2015c   46      4
## KI2016a   21      4

Plot unique Symbiont types by coral taxa

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## [1] 14
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Principal and Background Types

Background Symbiodinium types are those which have <0.01% abundance, and Principal Symbiodinium types are those which ahve >0.01% abunance (per Quigley et al 2017).

Abundance vs. Prevalence

Rank Abundance Curves - all timepoints

Rank Abundance Curves - before and after (alive/dead corals only)

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## Using Abundance as value column.  Use the value argument to cast to override this choice
## Using Abundance as value column.  Use the value argument to cast to override this choice
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